The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

International health regulations and pre-travel health practices of international travelers at Nigerian airport: a cross-sectional study

Abstract Background International Health Regulations (IHR) were developed by the World Health Organization (WHO) to curb the trans-border spread of epidemics. To our knowledge, no airport-based studies have assessed travelers’ health practices against a combination of diseases subject to IHR 2005. Therefore, we aimed to generate and describe the baseline travelers’ pre-travel health practices towards Cholera, Yellow Fever (YF), and Plague at Murtala Muhammed International Airport (MMIA) in Nigeria. Methods A cross-sectional study was employed to collect data from 486 international travelers using a multistage sampling technique. Pre-travel health practices (a combination of pre-travel consultation, pre-travel vaccination, and preventive measures against insect bites) were assessed using an interviewer-administered questionnaire. Logistic regression models were used to estimates the association between selected variables and pre-travel health practices. Statistical significance level was set at 5%. Results A total of 479 complete questionnaires were analyzed. The median age of respondents was 34.0 years Interquartile range (IQR) = 28.0, 44.0). Of the total respondents, 311 (64.3%) were aware of pre-travel health consultation and sources of information, amongst others, including friends/relatives in 180 (37.6%) travelers, social media/internet in 155 (32.4%) travelers, and health professionals in 102 (21.3%) travelers. Two hundred and seventy-one (56.6%) had pre-travel consultation, 156 (32.6%) had YF vaccination, and 226 (47.2%) were prepared to use preventive measures against insect bites. Only 10.6% had good pre-travel practices against the diseases subject to 2 International Health Regulations (IHR). Travelers with bachelor/college degrees, when compared to those with secondary/high education, had 2.91 times higher odds of having good practices when adjusting for other factors (95% C.I: 1.10, 7.70; p < 0.03). Also, those traveling to destinations endemic for YF infection, when compared to those who are not traveling to endemic countries/areas, had 48% lower odds of having good practices after adjusting for other factors (95% C.I: 1.41, 7.77; p < 0.01). Conclusions Our study revealed a low prevalence of good pre-travel health practices among participants. Educational level and endemicity of YF at the destination were predictors of pre-travel health practices. Introducing topics on travelers’ health into schools’ curriculums may have a ripple positive effect on health practices among international travelers. Also, there is a need for public enlightenment programs on pre-travel health practices using social media platforms